Fish aggregation devices (FADs) have been used extensively in the tuna purse seine fishery since the 1980s. This long-term modification of natural habitat has generated discussions as to whether FADs impact movement patterns of tuna species. We examined this question using data collected from the skipjack tuna (Katsuwonus pelamis) fishery. We used the longitudinal gravitational center of catch (G) to examine temporal variability in skipjack movement in the Western and Central Pacific Ocean, and related this to El Niño Southern Oscillation (ENSO) events. We found that in most cases G for free-swimming school sets changed with the onset of ENSO events, while G for floating-object-associated school sets remained relatively constant. This suggests that skipjack exhibit distinguishable behavioral strategies in response to ENSO events: they either react by moving long distances or they associate with floating objects. There has been no previous attempt to evaluate the interaction between FADs and the environmentally-determined movement of skipjack; this study shows evidence of an interaction, which should be considered when managing skipjack populations.